I can't see all my gear in the melding interface

[HarryTipper]

I will use my bad memory to help you, so it's propably because fully melded items do not show up in that menu?

Pretty much this.

After looking at your gear on Lodestone, the other gear pieces still show up because those are crafted items.
Those can be overmelded beyond the 2 standard Materia slots (1 for Accessories) up to 5, that's why they still show up in the menu.

If you want to remeld your gear, you will have to remove materia first and then meld again.